Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. (November 2018)

• Record Type: Journal Article
• Authors: Zhang, Jisen; Zhang, Xingtan; Tang, Haibao; Zhang, Qing; Hua, Xiuting; Ma, Xiaokai; Zhu, Fan; Jones, Tyler; Zhu, Xinguang; Bowers, John; Wai, Ching; Zheng, Chunfang; Shi, Yan; Chen, Shuai; Xu, Xiuming; Yue, Jingjing; Nelson, David; Huang, Lixian; Li, Zhen; Xu, Huimin; Zhou, Dong; Wang, Yongjun; Hu, Weichang; Lin, Jishan; Deng, Youjin; Pandey, Neha; Mancini, Melina; Zerpa, Dessireé; Nguyen, Julie; Wang, Liming; Yu, Liang; Xin, Yinghui; Ge, Liangfa; Arro, Jie; Han, Jennifer; Chakrabarty, Setu; Pushko, Marija; Zhang, Wenping; Ma, Yanhong; Ma, Panpan; Lv, Mingju; Chen, Faming; Zheng, Guangyong; Xu, Jingsheng; Yang, Zhenhui; Deng, Fang; Chen, Xuequn; Liao, Zhenyang; Zhang, Xunxiao; Lin, Zhicong; Lin, Hai; Yan, Hansong; Kuang, Zheng; Zhong, Weimin; Liang, Pingping; Wang, Guofeng; Yuan, Yuan; Shi, Jiaxian; Hou, Jinxiang; Lin, Jingxian; Jin, Jingjing; Cao, Peijian; Shen, Qiaochu; Jiang, Qing; Zhou, Ping; Ma, Yaying; Zhang, Xiaodan; Xu, Rongrong; Liu, Juan; Zhou, Yongmei; Jia, Haifeng; Ma, Qing; Qi, Rui; Zhang, Zhiliang; Fang, Jingping; Fang, Hongkun; Song, Jinjin; Wang, Mengjuan; Dong, Guangrui; Wang, Gang; Chen, Zheng; Ma, Teng; Liu, Hong; Dhungana, Singha; Huss, Sarah; Yang, Xiping; Sharma, Anupma; Trujillo, Jhon; Martinez, Maria; Hudson, Matthew; Riascos, John; Schuler, Mary; Chen, Li-Qing; Braun, David; Li, Lei; Yu, Qingyi; Wang, Jianping; Wang, Kai; Schatz, Michael; Heckerman, David; Sluys, Marie-Anne; Souza, Glaucia; Moore, Paul; Sankoff, David; VanBuren, Robert; Paterson, Andrew; Nagai, Chifumi; Ming, Ray;
• Is Part Of: Nature genetics. Volume 50:Number 11(2018)
• Page Start: 1565
• Page End: 1573
• Publication Date: 2018-11
• Subjects: Human genetics -- Periodicals; 576.505
• DOI: 10.1038/s41588-018-0237-2
• Languages: English
• ISSNs: 1061-4036

Abstract

Abstract Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content fromSaccharum officinarum with hardiness, disease resistance and ratooning ofSaccharum spontaneum . Sequencing of a haploidS. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35, 525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 inS. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. IntrogressedS. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in differentS. spontaneum accessions. The allele-definedSaccharum genome offers new knowledge and resources to accelerate sugarcane improvement. Sequencing of haploid sugarcane, Saccharum spontaneum, allows assembly of a prototypical version of the sugarcane chromosome set. This new reference genome will serve as a resource to accelerate sugarcane improvement.